New Biological Route for Swine Flu to Human Infections

Berkeley Lab researchers have discovered a new biological pathway by which the H1N1 flu virus can make the jump from swine to humans. Early tests indicate this pathway may have played an important role in transmitting the virus into humans.

A new biological pathway by which the H1N1 flu virus can make the jump from swine to humans has been discovered by researchers with the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California, Berkeley. Early test results indicate that a heretofore unknown mutation in one of the H1N1 genes may have played an important role in transmitting the virus into humans.

“Transmission of influenza viruses into the human population requires surmounting biological barriers to cross-species infection,” says biochemist Jennifer Doudna, the principal investigator for this research. “We have identified an adaptive mutation in the swine origin H1N1 influenza A virus – a pair of amino acid variants termed the ‘SR polymorphism’ – that enhance replication, and potentially pathogenesis of the virus in humans.”

A mutation in the H1N1 influenza A virus, termed the SR polymorphism, enhanced replication of the virus in humans. (Image courtesy of NIGMS)

Doudna, an authority on RNA molecular structures, holds joint appointments with Berkeley Lab’s Physical Biosciences Division, and UC Berkeley’s Department of Molecular and Cell Biology and Department of Chemistry. She’s also an investigator with the Howard Hughes Medical Institute (HHMI). She and Andrew Mehle, a post-doctoral fellow in her research group, have published a paper on this research in the Proceedings of the National Academy of Sciences (PNAS) titled: Adaptive strategies of the influenza virus polymerase for replication in humans.”

“Our work highlights the importance of basic research in understanding the processes that control emergence of new influenza viruses,” Mehle says. “For example, we now have a new genetic marker to monitor that might help predict the ability of influenza viruses to enter the human population.”

One way in which an influenza virus surmounts biological barriers to cross-species infection is through a mutational change in its polymerase, the enzyme that enables the virus to replicate. Identifying such mutations is a key to preventing influenza pandemics or devising new vaccines against infections. When a host is infected with an influenza virus, the polymerase enables the virus to multiply in the host’s cells by making copies of the viral genome and directing production of its proteins. Disrupting polymerase function can stop the virus from replicating and thereby reduce the spread and severity of an infection.

“The processes regulating emergence of viruses into the human population involve a complex interplay between virus and host,” Doudna says, “and understanding the mechanisms by which influenza viruses acquire the ability to infect multiple species is imperative to controlling future outbreaks. Transmission of the influenza virus into a new species can be influenced by mutations in any of the virus’s eight genes.”

The influenza polymerase consists of three proteins dubbed PB1, PB2 and PA, that work with viral RNA and nucleoprotein to transcribe and replicate the influenza genome in a host cell. Earlier work by Doudna and Mehle with avian influenza had shown that a mutation in the viral protein PB2 – whereby glutamic acid is replaced at a certain position on the amino acid chain with lysine – enables the virus to jump from birds to humans. When glutamic acid is retained in PB2, its presence suppresses the polymerase from performing in human cells.

“That’s why we were surprised when we looked at the gene sequences for the current H1N1 polymerase,” Mehle says. “The viruses were replicating in people yet they retained the inhibitory glutamic acid in PB2.”

In their investigation, Mehle and Doudna found that the 2009 H1N1 virus has acquired the SR polymorphism in its PB2 protein that enhances polymerase activity in human cells. To confirm that the SR polymorphism was a new pathway for the virus to infect humans, they introduced the mutation into the PB2 protein of the avian influenza. As with swine influenza, the polymerase activity and viral replication of the avian virus became enhanced in humans.

Andrew Mehle (Photo by Roy Kaltschmidt, Berkeley Lab Public Affairs)

“The SR polymorphism mutation in PB2 accomplishes the same goal as the change from glutamic acid to lysine,” Mehle explains. “The fact that all of the 2009 H1N1 isolates contain this second mutation supports the notion that it is important for transmission into humans, although we don’t yet know the relative importance of the changes in the polymerase versus mutations elsewhere in the virus.”

Mehle and Doudna are now conducting a series of biochemical and structural studies to get a comprehensive understanding of this polymerase mutation and why it evolved. Such studies are necessary before effective new antivirals can be developed.

“We need to identify what is unique about human cells that requires mutations in the influenza polymerase, possibly providing new avenues to exploit in developing therapeutic strategies,” Mehle says.

This research was supported by supported by the National Institutes of Health through its National Institute of General Medical Sciences programs.

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